function `findOverlaps()` is not found for region-based analysis

i am going through your RcisTarget tutorial for region based parts of the genome so I can apply it to my ATAC-seq dataset RcisTarget tutorial. I am using R version 4.1.1 and have confirmed I have RcisTarget version 1.12.0 as the tutorial suggests.

Everything runs fine until I run the following in of code in the tutorial:

regionSets_db <- lapply(regionSets, function(x) convertToTargetRegions(queryRegions=x, targetRegions=dbRegionsLoc))

It seems that the convertToTargetRegions() function relies on the function findOverlaps() which does not exist within the proper scope.

The exact error message is as follows: Error during wrapup: could not find function "findOverlaps"

For full transparency and reproducibility here is the sessionInfo():

R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /home/tonya/R/x86_64-pc-linux-gnu-library/R-4.1.1/lib/libRblas.so
LAPACK: /home/tonya/R/x86_64-pc-linux-gnu-library/R-4.1.1/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] AUCell_1.14.0     RcisTarget_1.12.0

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.4.3        Biobase_2.52.0              httr_1.4.2                  bit64_4.0.5                
 [5] R.utils_2.10.1              shiny_1.6.0                 assertthat_0.2.1            BiocManager_1.30.16        
 [9] stats4_4.1.1                blob_1.2.2                  GenomeInfoDbData_1.2.6      Rsamtools_2.8.0            
[13] yaml_2.2.1                  pillar_1.6.2                RSQLite_2.2.8               lattice_0.20-44            
[17] glue_1.4.2                  digest_0.6.27               GenomicRanges_1.44.0        promises_1.2.0.1           
[21] XVector_0.32.0              htmltools_0.5.2             httpuv_1.6.2                Matrix_1.3-4               
[25] R.oo_1.24.0                 GSEABase_1.54.0             XML_3.99-0.7                pkgconfig_2.0.3            
[29] zlibbioc_1.38.0             purrr_0.3.4                 xtable_1.8-4                later_1.3.0                
[33] BiocParallel_1.26.2         tibble_3.1.4                annotate_1.70.0             KEGGREST_1.32.0            
[37] generics_0.1.0              IRanges_2.26.0              ellipsis_0.3.2              cachem_1.0.6               
[41] SummarizedExperiment_1.22.0 BiocGenerics_0.38.0         magrittr_2.0.1              crayon_1.4.1               
[45] mime_0.11                   memoise_2.0.0               R.methodsS3_1.8.1           fansi_0.5.0                
[49] graph_1.70.0                tools_4.1.1                 data.table_1.14.0           BiocIO_1.2.0               
[53] lifecycle_1.0.0             matrixStats_0.60.1          S4Vectors_0.30.0            DelayedArray_0.18.0        
[57] AnnotationDbi_1.54.1        Biostrings_2.60.2           compiler_4.1.1              GenomeInfoDb_1.28.2        
[61] rlang_0.4.11                grid_4.1.1                  RCurl_1.98-1.4              rstudioapi_0.13            
[65] rjson_0.2.20                bitops_1.0-7                arrow_5.0.0                 restfulr_0.0.13            
[69] DBI_1.1.1                   R6_2.5.1                    GenomicAlignments_1.28.0    dplyr_1.0.7                
[73] rtracklayer_1.52.1          fastmap_1.1.0               bit_4.0.4                   utf8_1.2.2                 
[77] parallel_4.1.1              Rcpp_1.0.7                  vctrs_0.3.8                 png_0.1-7                  
[81] tidyselect_1.1.1

aertslab / RcisTarget

function `findOverlaps()` is not found for region-based analysis #23